LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.

# ------------------------ INITIALIZATION ----------------------------

units 		metal
dimension	3
boundary	p	p	p
atom_style	full

# ----------------------- ATOM DEFINITION ----------------------------

fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
Reading data file ...
  orthogonal box = (0 0 0) to (24.09597 24.09597 24.09597)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  432 atoms
  scanning bonds ...
  1 = max bonds/atom
  orthogonal box = (0 0 0) to (24.09597 24.09597 24.09597)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  216 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     1 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.004 seconds

group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells

neighbor 2.0 bin
comm_modify vel yes

# ------------------------ FORCE FIELDS ------------------------------

pair_style   born/coul/wolf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl

bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0

# ------------------------ Equilibration Run -------------------------------

reset_timestep 0

thermo 50
thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol

compute CSequ all temp/cs cores shells

# output via chunk method

#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector

thermo_modify temp CSequ

# velocity bias option

velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 22
  ghost atom cutoff = 22
  binsize = 11, bins = 3 3 3
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair born/coul/wolf/cs, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
velocity all scale 1427 temp CSequ

fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ

# 2 fmsec timestep

timestep 0.002
run 500
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.131 | 7.131 | 7.131 Mbytes
   Step         TotEng         PotEng         KinEng          Temp          Press          E_pair         E_vdwl         E_coul         E_long         E_bond         Fnorm           Fmax          Volume    
         0  -637.41039     -677.06805      39.657659      1427          -21302.622     -677.06805      1.6320365     -678.70009      0              0              1.3530839e-14  3.6429193e-15  13990.5      
        50  -635.62704     -667.67108      32.044047      1153.0397     -4532.6842     -669.45828      37.771018     -707.2293       0              1.787201       9.6848095      2.2028349      13990.5      
       100  -632.76343     -662.83014      30.066711      1081.8893     -3493.0827     -664.98212      39.195967     -704.17809      0              2.151977       11.060773      2.1578583      13990.5      
       150  -630.82533     -663.70172      32.876385      1182.9897     -75.706973     -666.12608      46.261038     -712.38712      0              2.4243598      11.746728      2.7663319      13990.5      
       200  -629.15463     -664.55009      35.395466      1273.6337     -1707.9185     -666.88117      41.794868     -708.67604      0              2.331082       10.596229      3.0031523      13990.5      
       250  -627.86625     -662.60876      34.742511      1250.1384     -1263.5726     -665.214        43.005742     -708.21974      0              2.6052329      10.572641      1.8416041      13990.5      
       300  -627.10829     -664.12159      37.013298      1331.8481     -1884.8587     -666.39136      40.786141     -707.1775       0              2.2697693      9.4160684      1.247227       13990.5      
       350  -626.2729      -665.01858      38.745682      1394.1844     -1433.1302     -667.44315      41.864785     -709.30793      0              2.4245625      10.312641      1.9815612      13990.5      
       400  -625.54274     -661.84438      36.301638      1306.2404     -355.45544     -664.4483       44.370671     -708.81897      0              2.6039277      11.076154      2.1819702      13990.5      
       450  -624.88802     -661.12299      36.234964      1303.8413     -2356.6102     -663.6463       39.57847      -703.22477      0              2.523314       9.8995886      1.3113549      13990.5      
       500  -623.86344     -660.20235      36.338906      1307.5814      462.72862     -662.8515       45.983055     -708.83455      0              2.6491489      10.523732      1.6709562      13990.5      
Loop time of 1.06095 on 4 procs for 500 steps with 432 atoms

Performance: 81.437 ns/day, 0.295 hours/ns, 471.277 timesteps/s, 203.592 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.89614    | 0.93939    | 0.9858     |   3.5 | 88.54
Bond    | 0.00018633 | 0.00020278 | 0.00021792 |   0.0 |  0.02
Neigh   | 0.016447   | 0.01646    | 0.016474   |   0.0 |  1.55
Comm    | 0.05532    | 0.10172    | 0.14501    |  10.7 |  9.59
Output  | 0.00013419 | 0.00014796 | 0.00018849 |   0.0 |  0.01
Modify  | 0.0017352  | 0.0017995  | 0.0018875  |   0.1 |  0.17
Other   |            | 0.001231   |            |       |  0.12

Nlocal:            108 ave         112 max         106 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost:        6531.75 ave        6611 max        6460 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:        74316.2 ave       75641 max       72780 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 297265
Ave neighs/atom = 688.11343
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0

unfix thermoberendsen

# ------------------------ Dynamic Run -------------------------------

run 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.133 | 7.133 | 7.133 Mbytes
   Step         TotEng         PotEng         KinEng          Temp          Press          E_pair         E_vdwl         E_coul         E_long         E_bond         Fnorm           Fmax          Volume    
       500  -623.86344     -660.20235      36.338906      1307.5814      462.72862     -662.8515       45.983055     -708.83455      0              2.6491489      10.523732      1.6709562      13990.5      
       550  -623.95339     -660.07946      36.126069      1299.9229     -362.67287     -662.8047       44.180832     -706.98553      0              2.725239       11.07199       2.0461377      13990.5      
       600  -624.04508     -661.27298      37.227902      1339.5701      110.39826     -663.90927      45.166569     -709.07584      0              2.6362912      11.747923      2.1846827      13990.5      
       650  -623.9608      -661.50573      37.544934      1350.9779     -1594.4701     -663.91531      41.226571     -705.14188      0              2.4095736      10.022027      1.6264012      13990.5      
       700  -624.00658     -663.55636      39.549777      1423.1181     -588.97998     -665.88666      43.124024     -709.01068      0              2.330298       9.924587       2.1027838      13990.5      
       750  -623.99813     -659.97695      35.978819      1294.6244     -364.14226     -662.75959      43.973554     -706.73315      0              2.7826459      11.487832      1.8799688      13990.5      
       800  -624.01235     -661.04909      37.036732      1332.6913     -85.656573     -663.49204      44.570114     -708.06215      0              2.4429544      11.213145      1.6792904      13990.5      
       850  -624.02581     -659.39933      35.373528      1272.8443     -1090.9203     -662.1197       42.375057     -704.49476      0              2.7203668      11.214627      2.2907455      13990.5      
       900  -624.09244     -663.33385      39.241411      1412.0222      303.75688     -666.00592      45.332449     -711.33837      0              2.6720671      11.897195      2.0599089      13990.5      
       950  -624.04544     -661.11576      37.070316      1333.8998      1637.6643     -663.61303      48.658973     -712.272        0              2.4972708      12.343808      2.4292102      13990.5      
      1000  -623.95457     -661.51814      37.563572      1351.6486     -851.7872      -663.83593      42.813436     -706.64936      0              2.3177834      10.251436      1.6922806      13990.5      
      1050  -623.98732     -662.01993      38.032615      1368.5261     -2123.9174     -664.72613      39.917351     -704.64349      0              2.706203       9.6007933      1.7366304      13990.5      
      1100  -623.9653      -659.32007      35.354771      1272.1694     -436.80378     -662.14438      44.058036     -706.20242      0              2.8243073      11.267638      2.680725       13990.5      
      1150  -624.02273     -665.13911      41.116373      1479.4888     -128.15352     -667.47701      44.013704     -711.49071      0              2.3379051      10.406577      1.5103886      13990.5      
      1200  -623.9733      -663.07995      39.106645      1407.1729     -539.60915     -665.67903      43.31939      -708.99842      0              2.5990769      10.63266       1.4610051      13990.5      
      1250  -623.92531     -661.81838      37.893067      1363.5048      1708.1374     -664.63564      48.397159     -713.0328       0              2.8172564      11.370051      1.8850128      13990.5      
      1300  -623.99378     -662.19802      38.204241      1374.7017     -820.60148     -664.34615      42.656636     -707.00278      0              2.1481249      10.185803      1.7067304      13990.5      
      1350  -623.99782     -658.71087      34.713048      1249.0783      774.2829      -662.01972      46.921079     -708.94079      0              3.3088484      12.45883       2.5036927      13990.5      
      1400  -623.96922     -662.14896      38.179736      1373.82        887.83381     -664.8944       46.646797     -711.5412       0              2.7454414      11.921113      3.051763       13990.5      
      1450  -623.95104     -662.24078      38.289741      1377.7783     -388.25212     -664.7512       43.653615     -708.40481      0              2.5104165      10.472699      1.8837175      13990.5      
      1500  -624.00697     -661.49681      37.489838      1348.9954      421.21197     -664.32938      45.681045     -710.01043      0              2.8325737      11.637595      2.0817672      13990.5      
Loop time of 2.1287 on 4 procs for 1000 steps with 432 atoms

Performance: 81.176 ns/day, 0.296 hours/ns, 469.771 timesteps/s, 202.941 katom-step/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.8623     | 1.9062     | 1.9457     |   2.2 | 89.55
Bond    | 0.00037699 | 0.00039683 | 0.00042027 |   0.0 |  0.02
Neigh   | 0.037117   | 0.037163   | 0.037221   |   0.0 |  1.75
Comm    | 0.14161    | 0.18101    | 0.22468    |   7.3 |  8.50
Output  | 0.00028467 | 0.00030487 | 0.00035281 |   0.0 |  0.01
Modify  | 0.0006751  | 0.00070515 | 0.00075299 |   0.0 |  0.03
Other   |            | 0.002961   |            |       |  0.14

Nlocal:            108 ave         116 max         102 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost:         6504.5 ave        6624 max        6380 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs:        74261.2 ave       79232 max       70984 min
Histogram: 2 0 0 0 0 1 0 0 0 1

Total # of neighbors = 297045
Ave neighs/atom = 687.60417
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:03
